Capsize or sink?
As long as you're talking about a small boat, capsizing is relatively easy, especially with more than one person involved and the goal is shared. Just rock it enough and the boat can be turned over, even with a motor, though they'd want that to be not running when they're doing it. Remember, capsizing just turns the boat over; turn turtle, as they say.
Sinking is more challenging. Perhaps three people could do it, but these things are designed not to sink. Getting enough water into it to weigh it down substantially would take time. If your characters capsize it and they're in the water, too, they'll have a hard time getting the leverage to get the boat at an angle that enables enough water to go in, and again, you have a motor attached, and that weight will not help them unless they're trying to sink it from the back, and that's the hardest place to do so, since that's the widest.
Now, a shotgun blast through the bottom might make it easier, but even then it depends on the size of the hole if you're trying to get the boat down quickly. Bigger hole would require a bigger blast, which is more likely to attract attention. Too small a hole and it would simply take too long for enough water to flow in to weigh down the boat. It's a matter of surface area.
I'm not sure what your characters' motivation is, so that presumably would play a role, too. Are two characters conspiring to kill the third? Are they working together to fool someone into thinking the three of them are dead? Is one of them captured and trying to escape? Lots of possibilities.
Neat question. It got my mind awhirl!