I missed the part where you need to slide the 3x3 tubes under the boat that's supported by 4x4 timber. Side-by-side is what you can accommodate.
HSS 3x3x3/16 Ix=2.6 in^4, Sx=1.73 in^3
Deflection of a single beam with a point load at center span, and the ends simply supported, is Pl^3/48EIx, so with the full 3500 lb on a single tube, you get (3500*140^3)/(48*30E6*2.6)=2.56 inches of deflection. Doubling the number of beams halves the deflection, and the bending stress, assuming they're sharing the load equally.
But, two beams together with the whole weight of the boat on it (3500 lb) is right up against the yield strength of the material. You'd need 4 or more such beams to carry the load with a reasonable factor of safety. Deflection would be 1/4 of that above, or about 5/8". Bending stress for the same configuration is Pl/4Sx, or (3500*140)/(4*1.73)=71 ksi, nearly double the minimum yield strength of 36 ksi of those tubes. 4 tubes would be a minimum.
Since you're laying them side-by-side, there is no value in continuous welds down both sides for the whole length. You just need to be sure they're both carrying the whole load together, especially at/near the center of the span, and at the ends, though supporting them on common timber at the ends should ensure they're sharing the load well at each end.
Use the above mental exercise at your own risk. Without seeing the project, boat, supports, knowing the steel grade for fact, etc., this is just messing about with numbers (and boats). Be careful, and if, whatever you end up doing, doesn't feel right, Don't Do It!.
Edit: Looking yet again, I see you have two beams at each end of the keel, presumably sharing the 3500 lb total displacement of the boat. That sounds reasonable, assuming the load is shared equally between each pair (or more) of tubes. Stitching them together will increase the lateral stiffness, but a bit of bracing is still probably a good idea, as RichH alluded to above.