Re: Wife insists on a manual transmission
2005 - 2012 Subaru outbacks have a 6 speed manual trans option with the H6 engine. (256 hp, 247 ft/lb torque) and are rated for 3,000 lbs. Finding one on the other hand... People don't get rid of subaru's, ever!
2011 Subaru Outback 3.6 R 4dr All-wheel Drive Wagon Specs (performance tab)
I'm a manual transmission lover and recently searched for new vehicles with manuals.
In the US, there is no such thing as an H6 Outback with a manual transmission from the factory. If there was the option of the H6 in 2012, I would've have ordered one then instead of my 2013 Outback 2.5 (manual trans of course).
The 4 cylinder Outbacks actually have a higher towing capacity then the 4 cylinder CVT Outbacks (2,700 pounds vs 2,000 pounds). It is to prevent overheating with the CVT's. With that being said, first gear in the manual trans is already questionably too high for the weight of an unloaded Outback. It would be an absolute beast on a steep boat ramp with a 2,700 pound boat (or any 1,000+ pound boat for that matter). The clutch would have to take a beating to get it done. Please don't take this to mean that I don't like my Outback. I actually like it a lot. It is an awesome all-around car but it would suck for as a 2,700 pound boat tow'er.
As others have said, a Jeep Wrangler can be had in a manual transmission. Unfortunately, the max listed towing capacity for new models is only 2,000 pounds. It seems to be less than the previous generations of Wranglers but I could be wrong.
Another option for a manual transmission tow vehicle would be a Toyota Tacoma. The max towing capacity of the 4.0 V-6 with manual trans is 3,500 pounds, so it is doable for you but not by much.
Also from Toyota is the FJ Cruiser with a manual. It would be a little more money than the Taco but it can tow up to 5,000 pounds. Unfortunately, the FJ has the love it or hate it look.
Out of these options, the FJ would probably suit your needs the best (of course, this is just based on towing capacities with manual transmissions).
Finally, you could spend a fortune and get a Dodge 2500 or 3500 diesel with a manual transmission, but that would be extreme overkill for your towing needs.
Edited to Add: I forgot about the Xterra in my research. It may or may not suit your needs, I don't know. I personally would never buy a Nissan because I strongly disagree with their engineering on their cars (absolute beasts to fix). I always figured some of their worthless engineering would transfer over into their pickups and SUV's but I could be wrong.