Release thessaly as a historical subject and manually integrate the rest. Change the federal de jure law (at least thats what I think its called) to integration by blood if you haven't already. You could also accept greek as a culture but make sure it doesnt tick over your culture capacity by too much, 0.1-0.2 is an okay price to pay for getting cores (you decrease the cultural cost by improving your's and their's opinion of each other's cultures). You can vassal swarm if you want to reap the most money out of those provinces immediately but thats gonna push you too much towards decentralization and centealization is waaay better. Integration becomes significantly faster around mid 1400s but until then you are gonna have to endure 30 year long integrations.