No, they're not the same.
"You'd better come with me." can mean "It would be better if you came with me" ie. "It is to your advantage if you came with me". This statement is just friendly advice. Or, if you said it in the wrong tone, it can sound like an implied threat or warning. ie "You will come with me, or else there will be consequences."
"It'd be nice if you came with me." is a polite or friendly invitation for someone to come with you. You are not advising them to come with you (or warning them to come with you) as with the first sentence.