Electrical Problems!!!

I went through some big mud puddles on saturday and my alternator went out. I went and got another one put it in everything was fine. I went and got a new battery yesterday was running great. I do some running around and i get out and smells like somthing is burning. I open the hood the the big black wire on the top of alt. is is smoking a little not alot right where it gose onto the alt. Theres no engine light on and its charging fine whats going on?

More than likely the connector is corroded and causing a high resistance, which then causes it to get hot as the current is generated to charge the battery. Clean or replace the connector.