Grounding options between three PCB's
In any circuit, current has to return back to the source and it will take the lowest impedance pathway to do so. So lets look at your circuit, you didn't really specify how the 3rd board functions which is important. There are problems that you will run into which may or may not be a problem for you. There is also no information on secondary cables that might be attached to the board.

If you are planning on sending this design through regulatory compliance testing or an FCC cert, you will have potential problems. If you have sensitive analog electronics, this design will also have potential issues.
If you don't plan on any testing, as long as you don't have too much ripple you should be mostly fine. 

1) If you connect the boards you will form a ground loop with your cabling with the grounds, to reduce this problem you will need to minimize the loop area AND reduce the impedance between boards 1,2 and 3 as much as possible. This means keeping the cables short, and the distance between the boards close. Use a thicker gauge wire to keep the impedance between the boards lower (to reduce common mode noise).

2) If you don't connect the grounds you will have a nice dipole antenna. 

There are also some things you can do to mitigate these problems, to prevent high frequency noise from getting to the DC to DC converters and onto your board, you could use a ferrite on the cable (increasing the inductace and thus increasing the high frequency impedance)

Another way to test this is to stitch the two ground planes together in several places with 0 ohm resistors, if one way works better than the other you can leave them or remove them. The more resistors you have in more places the better off you will approximate a connected ground plane. This is not exactly the same as having a sold ground plane as it will add a few nH's of inductance and mΩ's of resistance between the planes but it works great for testing.

EMC is an art, because most of it depends on parasitics and circuit elements that are difficult and impossible to measure. Something that might work for one design may not work well for another because of the small details. A good way is to plan for this in the design phase and come up with good testing methods.