If you plan it right, you might be able to tow the boat with your car.
I have the Lexus GX470 (a Toyota 4Runner, only with a V8) and my "side tow" vehicle is a 97 F150. The GX470 is my daily driver, and I actually find myself towing my AR210 with that 99% of the time. There's no real reason for this other than I keep the F150 at our vacation place, and we currently pick the boat up from storage at the halfway point between houses. This coming season, the boat will be stored at the vacation place, and towing will likely switch to the F150.
I have no idea what the dimensions are of your garage, you didn't mention that, but I have a long-bed regular cab (no rear seating) that doesn't fit LENGTHwise into my 2-car garage due to storage racking at the front of my garage. Width-wise, there's zero issues with it fitting in the garage, as it's the same as my GX470. I pull straight in, the wife backs her car in, both driver's side doors open towards the other car, and we fit perfectly fine.
That tip about older F150's having issues with spark plugs breaking is no joke, just search Amazon for broken spark plug tools. There are things to mitigate the problem, but if you're buying used, you have no assurances the previous owner did anything to help you. Mine has the 4.6L, not saying there can't be issues with the spark plugs, but my engine is on the "low enough to be a non-issue" spectrum.
Mine is a 4x4. Absolutely sucks for mileage, but I don't think I'd want a 4x2 on a slippery boat ramp. Sucks for snow with regular tires, but with snow tires, I wouldn't hesitate to drive ANY vehicle in the snow. I have no idea what your mechanical aptitude is, but I've had snow tires for my last 3 RWD cars and the GX470, and I change them out when snow is forecast, and swap them back out - I have a garage full of tools that make this easier, and I don't mind doing this to get more life out of my snow tires - your mileage and experience may vary.
I'm not a fan of the F150 as a daily driver, but it's do-able. Cost of fuel and mileage are the reason I wouldn't do it. If you have the ability to do 3 vehicles, I'd keep your two current cars and park the truck for use as needed. My truck has always lived outside as long as I've owned it. It's a truck. If it were made out of tissue paper, I'd worry about it being outside all the time, but since you're looking at a modern vehicle, it will do just fine living out in the elements. Some things may age quicker, like the plastics, but you can get UV protectants, or just buy new plastics as they age out.
As for loading up stuff in the truck bed or not, that's up to personal choice, but I'm all about not loading my boat twice. I tow with the mooring cover on, so I don't have issues with things blowing out. I have a soft cover on the truck bed that rolls up when I need to use the bed, and I have no issues with it. My FIL had a hard tonneau cover, and there were some issues here and there, I'm sure it all depends on the cover you get/have, and that can always be swapped out for something that better fits your needs.
Last item, a few folks mentioned a backup camera.
I bought a wireless license plate camera from Costco. (click for link) $170 regular price. At that price, I wouldn't rule out anything that doesn't have a backup camera, as you can easily add one on.
My son is supposedly taking my F150 off my hands, and if he does, I'll be looking to pick up another GX and relegating the current GX to backup duty. I have trailers I can use, so I don't need a truck bed anymore, and I want all my vehicles to be able to fit in my garage. If you have a need for the truck bed, I wouldn't bother with a short bed. If you think you can deal with a short bed, then my opinion is to skip the truck altogether and get a 4Runner or a Lexus GX. I've had my share of Honda's in the past, IMO, Toyota does things a bit better. If you can find a good deal on a Tundra or Tacoma, they're both a great choice. If I could have found either at the same price/mileage ratio as my F150, I'd have never left the Toyota family.