Are Mutos extinct now

I mean as far as we know they are, but more could be found in other sinkholes in future installments of the series, so I wouldn't jump to conclusions

Possibly. In the bonus features, it said that there could be more out there. Well, I guess you could say there is, and MUTO is used to describe any Massive Unidentified Terrestrial Organism

Yeah, in the special features for the Mutos, they are described as the "U.F.O of monsters", so the name can apply to a vast range of creatures.

But the Muto creatures specifically from the 2014 movie may be extinct. 

In Godzilla: Awakening, Godzilla was described as a MUTO before they gave him a name

NERDYBANDGEEKS makes a point. Until the monster is given a name (such as Gojira/Godzilla, Mothra, Rodan, King Ghidorah) is is known as a M.U.T.O. So the Daikaiju species is not extinct, but those specific Muto (which I don't think Monarch or anyone else would rename) may very well be extinct. There could still be more fossilized remains of Daikaiju with Muto larva in them.

M.U.T.O is just an acronym, and you can't make an acronym go extinct. Godzilla is a M.U.T.O, in all likelihood, the first M.U.T.O. He has a name now, but is none the less still a Massive Terrestrial Organism. The only thing that changed was that he is now identified.

So no, the M.U.T.O's are not extinct as every Kaiju without a name or identification mark of any kind is considered a M.U.T.O.