There are two different issues here. (1) Is it a good approximation to describe a particular composite system as a boson or a fermion? (2) If so, which is it?
Question #2 is the easy one. The spin-statistics theorem tells us that iff the spin is an integer, the object is a boson. For an atom or ion, this is determined by whether the total number of electrons and quarks is even.
Question #1 is more complicated. Akhmeteli's answer has explained, based on general ideas about quantum mechanics, why the answer may be no. For an atom, I think this issue comes down to the energy/temperature regime you're dealing with and the strength of the interaction between the nucleus and the electrons (hyperfine interaction). If the nucleus didn't interact at all with the electrons, then it would be meaningless to consider them as a composite system. They do interact, but the interaction is very weak; it amounts to $\sim 10^{-4}$ eV, or about 1 K in terms of temperature.
At room temperature, we're dealing with temperatures hundreds of times higher than this scale, so any hyperfine effects are too delicate to matter. This is why, for example, the properties of 3He and 4He gases differ only due to their differing masses.
At temperatures below about 1 K, hyperfine effects start to matter. At these temperatures, 3He and 4He liquids differ qualitatively, because 4He is a boson, and it forms a superfluid due to effects analogous to Bose-Einstein condensation.
To make this more clear, it may be helpful to observe that there are two independent temperature scales here. The first one is the one described in the first paragraph above, the temperature corresponding to the strength of the hyperfine interaction. Let's call this $T_{hf}$. The second one is the temperature at which the de Broglie wavelength of the atom is equal to the typical spacing $n^{-1/3}$ between the atoms, where $n$ is the number density. Below this temperature, we expect the substance to be highly quantum-mechanical, so let's call it $T_q$. This temperature is given by $T_q=\hbar^2 n^{2/3}/2mk$. For superfluid 4He, this comes out to be about 0.4 K. For helium, these two temperatures happen to be about the same, but in principle they are completely separate. If we want to see any effect from quantum statistics, we need a temperature $\lesssim T_q$. It happens that for helium, this also guarantees that we're at temperatures low enough so that the nucleus couples to the system and affects the statistics, but that is an accident of nuclear physics, which happens to give magnetic dipole moments on a certain order of magnitude.
In general, it is not always correct to try to treat composite systems as elementary. It may or may not be a good approximation to do so. For example, in nuclear physics we can try to treat nucleons as elementary particles, and talk about two-body interactions between them, but this is messy and involves approximations, because really whe a nucleon interacts with another nucleon, it's just six quarks interacting. Similarly, it doesn't always make sense to attribute Bose or Fermi statistics to a composite system. At temperatures $\lesssim T_{hf}$, it makes sense approximately to treat an atom as a composite system whose statistics are defined by its total spin (nuclear coupled to electronic).
In a case like 4He where the nucleus has zero spin, there are two separate reasons why the nucleus doesn't affect the statistics. One is that the nucleus has integer spin, and adding an integer to another number doesn't affect whether it's an integer or a half-integer. The other reason is that a system with zero spin can't have a magnetic moment, so there's no way to couple it to the electrons magnetically, and therefore $T_{hf}$ is effectively zero.
[EDIT] Prompted by Lubos Motl's skepticism, I looked around for some more general treatment of the basic issue of whether, when, or to what approximation spin-statistics applies to composite systems. It turns out that the classic paper on this topic is Ehrenfest 1931. Unfortunately this scientific paper paid for by my grandparents' income taxes is behind a paywall, but here is the abstract:
From Pauli's exclusion principle we derive the rule for the symmetry of the wave functions in the coordinates of the center of gravity of two similar stable clusters of electrons and protons, and justify the assumption that the clusters satisfy the Einstein-Bose or Fermi-Dirac statistics according to whether the number of particles in each cluster is even or odd. The rule is shown to become invalid only when the interaction between the clusters is large enough to disturb their internal motion.
This makes it clear that the application of the spin-statistics theorem to composite systems is only an approximation. I can't be sure, because I haven't yet found a more complete presentation of the argument online, but the abstract quoted above does seem to be consistent with my analysis above of liquid 3He and 4He. At temperatures above $T_{hf}$, the interaction is "large enough to disturb" the "internal motion," i.e., the delicate hyperfine coupling of the nuclear spin to the electrons.
P. Ehrenfest and J. R. Oppenheimer, "Note on the Statistics of Nuclei," Phys. Rev. 37 (1931) 333, link.aps.org/doi/10.1103/PhysRev.37.333 , DOI: 10.1103/PhysRev.37.333