I've been twice. First year sat in the left-centerfield seats (would be the bleacher seats for a baseball game) to the left of the centerfield scoreboard if looking from home plate. I liked them (I sit in 327 in the Orange end zone upper deck at the Dome and it is a very similar perspective.) Was awesome to watch that flea-flicker play to Marcus Sales develop!
The second year we were Mezzanine level about halfway between third base and the left field wall. Good seats, too.
Personally, I would avoid all lower level seats on the lines. You are pretty distant from the field and the elevation of the seats doesn't allow for a good perspective, in my opinion.
If you do go, SU typically hires out Billy's Bar as it's home base. Get there early and enjoy the atmosphere. It is a blast.
I can honestly say that the first Pinstripe Bowl experience was one of the best, if not the best, sporting experiences I've ever had.