Without any text...
Yes, it's hard to fit 3 square figures on a page, especially if you don't have any text or anything else on it to balance everything. Your only other options than the ones you mentioned in your questions are to alternate your squares if you want to keep the same size.
If it's going to be printed at some point, even on an office laser printer, your example doesn't leave much room for the margin, a staple in the top corner, binding or anything like this. You will need to shrink your figures a bit OR put 2 figures per pages if you can.
It usually looks like this if you want to have big squares and play safe:
But if you can, the nicest way to add 3 square figures elegantly is to align them in the middle of the page, at smaller size.
Otherwise, use 2 figures per page, or 1.
If you're not obliged to have 3 figures per page, it's ok to have 2 on
one page, and a bigger one alone on another page. As long what you
want to represent with your graphics is visible. Simply make the one with the most details on its own page.
If you had text...
If you have some text, you can create all sort of effects to balance your 3 figures.
Maybe you could add the figure number or source as text to add a
little extra to your layouts.
Left aligned with compact text:
Right aligned with extended text area: