I was thinking about using finish screws instead of nails where necessary to surface nail, and in the tongue where the air nailer can't be used? I am thinking the screws will hold better. What do you think?

I've used trim head screws. When using on the surface I countersink and fill the small hole. How about a finish nail gun when the flooring nailer won't fit or is this the air nailer you are referring to? Hand nailing finish nails will work too and will provide sufficient hold....good idea to predrill when using on the surface.
One other thing....if you are surface nailing and you are close to an edge which has a groove and no tongue coming into it be very careful not to split the flooring board as there isn't much support.

Using a screw through the tongue like a blind nail is overkill. You would also need to pre-drill since the screw head would deform the tongue and make it hard to slide the next board into position. 8d casing nails are the best. If you can find blunt tipped nails, they will sometimes work without the pre-drilling, but pre-drilling at the right angle before the board gets installed is the easiest and will keep the tongue from splitting away from the board.

The screws worked great actually. I used GRK, 8x 2-1/2" fasteners I bought at Lowes. I did pre-drill the holes on the face as well as through the tongues. There was no splitting of deforming of the tongues whatsoever. I can't say the same for the cleats. I realize it is a slow process, but I would do it again without hesitation. Rock solid.

Glad to hear that you got good results. I've used GRK for different applications and really like them. SPAX makes some good screws too.