You can imagine that each EM wave spans, in space, an integer multiple of ~1 mm. In which case, if you divide the universe into a $1\times 1\times 1$ mm$^3$ grid, each cell will 'contain' an integer number of EM waves. So in order to fully describe the state of this simplified universe (containing only microwaves) you need the number $N$ of 1 mm$^3$ cubes that fill it (specifically, you would have $N$ integers, e.g. 0,0,1,9,0,2,..., that counts the number of EM waves/energy density in each cell).
Each cell therefore has an integer value that will obey some probability distribution $P:\mathbb{N}_0\to\mathbb{R}$ and will be capped at some maximum value $M$, i.e. $P(M > 0)=0$. So the number of microstates can be approximated by $M^N$, and thus the entropy will be in the region of $k_B\log(M^N)=k_B\log(M)N$.
The value of $N$ is $\sim 10^{90}$, which will dwarf $\log(M)$. So, in atomic units ($k_B=1$), $N$ is a good estimate for the entropy of the universe.