In Teramachi, this Ōbaku temple (Ōbaku is the third-largest Zen sect after Rinzai and Sōtō) was built in 1629 by Chinese monk Chaonian. Its red entrance gate (Daiippo-mon) exemplifies Ming-dynasty architecture. Inside the temple you can admire a huge cauldron that was used to prepare food for famine victims in 1681, and a statue of Mazu (aka Maso), goddess of the sea, worshipped by early Chinese seafarers. There are excellent descriptions in English throughout the grounds.
Sōfuku-ji
Top choice in Nagasaki