Those subs will need a dedicated box in either location, easiest to build it out of MDF and then coat it in fiberglass, or I would just build the entire thing out of fiberglass just due to the water environment n all. MDF and water absolutely do not mix.
Those subs are looking for 0.75ft^3 per sub, or 1.5ft^3 for the pair. Looks like from those pics you easily have that space in both locations. I honestly I don't put a lot of weight into sound quality on a boat, I feel it is more about output when on the water, so with that I personally would put the subs in the most convenient spot you can use, which seems like under the passenger seat.
I am not sure of the construction of the seat or the piece underneath it, but in a best case scenario it looks like you could remove the seat cushions and then build a box inside the base using the panel facing the aisle as the face of the box. Then you could just carefully cut/trim back the padded vinyl face to make the opening for the subs then you won't even need to recover that panel.
For sizing the box, if you measure up the area you have to work with, then start checking some numbers on this page you should be able to get the dimensions you need for the box to be 1.5ft^3
http://www.rockfordfosgate.com/Support/rftech.aspx#boxwizard