In the Doctor, after Regina took her first heart, Rumple met up with Whale and told him he’d made his monster. I doubt Whale would’ve hung around longer than necessary in the EF which would mean this episode was either before or after the Doctor.
Regina used her EQ voice when she told Tinkerbell to leave and she definitely began having dark thoughts about Snow without being horrified by them. I would say this was probably after the Doctor because Rumple said to bring her anger to the next lesson whereas she wasn’t angry when we saw her in the Doctor.