The three Kingdoms are:
Crownlands aren't a separate Kingdom historically but Jaime isn't the most well-versed guy in law. In the books it is noted many times that he is very dumb when it comes to history and Law. But then again, he could be referring to Stormlands instead but Stormlands are uncertain as well given that Cersei isn't a Baratheon and has no claim to the throne.
It can't be Iron Islands as at that time Jaime didn't know about
When he says "at best", he's mentioning the ideal scenario. If you are overly-optimistic and everything goes well, those are the only three Kingdoms Cersei has control over. But Jaime knows Riverlands are uncertain
given murder of the Frey family
and so are the Stormlands. Therefore he uses "At best".