It can tow for sure, but the gearing and final drive with the manuals is not ideal for low-speed towing (or crawling). It's still doable but the onerous will be entirely on you to manage your clutch properly, or else it is going to have a shorter life than it should. Thats really all there should be to say about it: If you suck at clutch-work you'll be having a new clutch installed sooner than you want to, and it will be your cost since its not Jeep's fault you killed it early. Other than that, tow away. There is no need to give worry about transmission coolers or oil temps and whatnot just to pull a little boat around every twice in a while.
Jeep is comfortable offering an overly-conservative official towing capacity number for the 9-speed automatic simply because the automatic makes it "idiot-proof" enough to keep the lawyers happy. (You should run the gears of the 9-speed manually, though, once you get up over 1000 lbs) With the manual, Jeep can't fool-proof it for you, the full responsibility of minimizing wear on the clutch and picking good gears that don't lug the engine is on you and they don't want to be left holding the bag for the type of people who can't handle that.
If and when you are at or around that 2000 lb mark on the highway, don't be afraid to keep a lower gear and higher RPM's. ~3000 RPM or even more with a really heavy load is not unreasonable, four-bangers don't have the torque to keep heavy loads at speed at low RPMs. Your instant gas mileage readout will be more useful than the temp gauge, the instant MPG figure can help you infer the overall amount of load on the engine to help with picking a gear. Odds are you won't use 6th gear unless your boat is extremely light. When I am pulling the really heavy trailers I don't typically get past 5th on the 9-speed.
Pulling a boat back up out of a boat ramp is going to be the least pleasant part, you may have to drive out slightly faster than a person would normally want to in order to avoid excessive clutch slippage but even that you should be able to do every weekend all summer if you want, and done properly the clutch should live a good long life, longer than a clutch that lives exclusively in a busy city with a ton of stop-and-go traffic.