Switching to 4.10's(if you don't already have them) would help with the towing, but it would probably cause your mileage to drop when not towing. You could go the other direction and gear for fuel economy, but that would hurt your towing capabilities.
If it were me, I'd start with an e-fan, exhaust, and SCT tuner. The tuner will hold three custom tunes, so you can have a torquey "tow" tune for the weekends with your jetski, and then switch to a "fuel economy" tune when you don't need to tow. Best of both worlds.
After that, if you're comfortable opening up your engine, there are a couple of sets of roller rockers (1.7's as well as 1.8's) available now that show nice gains in hp and tq. The reduced friction in the valvetrain might help out the fuel economy as well.
Should be able to do those mods for under $1200, then spend the rest on maintenance.