He had to have had say
Other wise why else would his son would not have been A.B.
And then his brother Peter was A.B. and then Boss

Neither one of them were boss material on their own merits.

I would say yes he was still in charge as much as one can be under the circumstances.

They managed to put out a hit on Gravano

According to Capeci and his sources Gotti was in control until the day he died.