In a way, Gotti's hands were tied. I'm sure Gotti was very aware of what Gravano was doing as shown in the tapes

But there were reasons why Gotti didn't act on them

Apart from being top guy in the family, Sammy had a big crew and was a big earner therefore to take him out wouldn't do Gotti much good

Not to mention, I'm sure Gotti was aware there were still many in the family who weren't happy with him taking out Paul Ie Castellano side. So by losing Gravano, that's one ally down in an event of a war

Which relates to the Westside, again Gotti was aware the Chin was causing problems and you need a guy like Sammy around just incase

so it was a question of tolerating what Sammy was getting up to or putting a complete stop to it which he didn't