It depends on the context. They both mean the same thing, but "ingratiate oneself with" is polite and formal language. "Suck up to" is very coarse language and it is clearly derogatory. So which one I would use depends on who I was talking to.
To my friend in the pub I could say "I reckon the President is sucking up to the Queen"
but if I was talking to the Queen, I would say, "I think that the President is trying to ingratiate himself with you, your Highness."