The pressure required will be the same in both cases. The force on the walls of the bottle is the pressure multiplied by the area, and assuming some uncrumple force $F_u$ is required to push the walls back into shape that means there will be some uncrumple pressure $P_u$ required. Whether that pressure is due to air or water makes no difference.
However the work required will be greater for air than for water. The work done in the process consists of:
the work needed to raise the pressure of the air or water to $P_u$
the work needed to uncrumple the bottle
The work required for part (2) will be the same for both air and water because the pressure is the same in both cases. In both cases the work will be:
$$ W_2 = P_u\,\Delta V $$
where $\Delta V$ is the volume increase of the bottle when you uncrumple it.
However because water is largely incompressible it takes negligable work to raise the water pressure to $P_u$ i.e.
$$W_1(\text{water})=0$$
By contrast air is compressible and it will take work for you to raise the pressure of the air from atmospheric to the uncrumple pressure $P$. Assuming air can be treated as an ideal gas, and ignoring changes in temperature the work done for air is:
$$ W_1(\text{air}) = nRT\ln\frac{V_0}{V_\text{bottle}} $$
where $V_0$ is the original volume of all the air you pushed into the bottle. That means the work for step (1) is greater for air than for water.