Which electric trolling motor is best, Minn Kota or MotorGuide? The funny part of the answer is that many of us won't get to choose. Most electrics get hard-mounted on the bow these days, and many manufacturers have OEM agreements with one company or the other. In some other situations, the decision is made for you because of the electronics you choose. Go with a Humminbird system, for example, and you'll need a Minn Kota at the bow in order for the units to talk to each other and take advantage of features like iPilot or Autopilot.
If you'll be transom-mounting, using a clamp-on mount at the bow, or are adding the motor to an existing boat, making the call will become a bit trickier (because you'll actually have to make it, and there are lots of choices). Both Minn Kota and MotorGuide offer a wide range of power (12, 24, and 36 volt models rated by pounds of thrust, equivalent to around a third of a horsepower to about three horsepower); a wide variety of mounting options; different types of foot, tiller, or remote controls; and both freshwater and saltwater models. And, just for the record, I've run a bunch of these from both companies, over the past two decades—dozens, in fact. And I've owned at least four different models from each company.
My impression? Honestly, they're neck-and-neck in quality, pricing, and functionality. And the electric trolling motors from both of these companies are surprisingly well-made.
Wait a sec—that sure sounds like an editorial cop-out, doesn't it? Yeah, I know. But I actually mean it. There's a Minn Kota Riptide in my shed that's been with me since I moved into this house in 2004, and I think it might date back to the 90s. Right next to it there's a Motorguide Great White that's nearly as old. Back around 2004 or 2005 I needed a 12-volt model and bought the cheapest one available, and that one still works just fine, too.
As for the other options out there... well many are knock-offs from brands no one's ever heard of, and buying one is a bad move. Quality is spotty at best, and trying to get them serviced is nearly impossible. If you're transom-mounting you do have some other reputable options (see Alternative Power: Outboards that are Gasoline Free for more information). But remember that these are intended as primary power sources, may require special battery systems, and aren't going to have the same electronic integration possibilities as dedicated trolling motors.
So how are you supposed to know which to choose? In this case, I think it's pretty darn simple: follow the path of least resistance. If you're attracted to an electronics system that matches up with either a Minn Kota or a MotorGuide, get that system and go with the flow. If you're buying a new boat and it comes with one brand or the other, don't let that stop you. And if it's a complete toss-up, shop around and take the best deal you can get. I'm pretty darn sure that either way—Minn Kota or Motorguide—you'll be happy with your electric trolling motor.