The last 2 times taking the boat out I have noticed the large reduction of power my trolling motor has. I now have to put it on the highest setting to be able to go anywhere, and even still it just barely trots along. I checked the connections to the two batteries and looked like a little corrosion. I cleaned the corrosion but the trolling motor is still weak. Both batteries that are hooked up to the trolling motor are fully charged and are good batteries. Is this a sign that the trolling motor is on its way out? Any ideas would be appreciated.

What is the voltage at the TM plug? You may have corrosion where the wires attach to the plug.
How do you know the batteries are good? Age, voltage after setting or just a good guess? Not being a SA but batteries can be bad even if new.

I haven't checked the voltage at the TM plug, I'm not 100% sure how to do that. I'll check to see if there is corrosion where the wires attach to the plug tonight.

The batteries are 2 years old this month and have sat for a few months with voltage still over 12.5V before I started taking the boat out a couple months ago. I guess I could take them out to get tested to be sure they are still good.

Probably the batteries. I had the circuit breaker go bad & that produced those symptoms. Check for monofiliment behind the prop.

I had the batteries tested and are both good batteries. The problem was that 1 battery was 30% and the other battery was around 68%. I hooked the batteries back up after them being charged and the trolling motor seems to have it's normal power back. So I'm going to replace the ancient onboard charger. Thanks guys!

Remember to always make sure you have at least 12.6V on a battery after it has settled down from being unhooked from a charger to be 100% charged.

I agree with this.

I finally did a bunch of 'battery learning' several months back to answer questions that I've had for a while. One of them being, "I've heard that the voltage has to be above 12V, but since it's a 12V battery, how much above 12V should it really be?" Turns out that the answer is 12.6 because 2.1 * 6 = 12.6. Each cell (there are 6 of them... like those 6 holes you check for water) produces 2.1V. Inside the battery, the cells are connected serially (which doubles voltages, not amp hours), so 12.6V is what you're looking for.

Surface voltage on the battery is only part of a way to test the batteries. Some batteries will show a good surface voltage until a load is placed on it. Load test the batteries and go from there.

Another thing to do is to get a $15 hydrometer; that measures the true state of the charge in a cell. I got one and printed out 10 copies of the same template where I can keep historical track of how each of the cells are doing. Keeping a historical log of the specific gravities in the cells is probably overkill and I'll give up on it sooner or later, but just having discovered that, it's kinda neat.

I found that both of my new TM batteries had one cell that on a full charge, had a smaller reading on the hydrometer than the others. Within the tolerance, but still quite a variance.

True for many, but not all lead-acid batteries. Some AGM's are 13.0v standing voltage at full charge.
For true deep cycle batteries, the only way to test them is a capacity test - not a basic load test.