They are similar terms. More common we would say, 'I agree with you' for a statement, and use 'I'll go along with you' for and idea or an action like doing something.

"I agree with you" means that my thinking about the issue is the same as yours. "I go along with you" can mean the same thing, and it can also mean that I may not agree with you, but I will follow what you want in this situation.