At the beginning of Venom, it's quickly established that Eddie Brock has history in New York. Anne Weying remarks that Eddie was "ran out" of the city after falling afoul of controversy, and even cites the Daily Globe specifically, the paper Brock worked at in the comics.
Venom may have established that Brock's stomping ground is San Francisco, but he only stayed there for a year or so in the comics. The rest of the time, he was busy chomping people's heads off in New York, and it's where the character should head to in the sequel.
While it remains to be seen just what happened to Brock in order for him to swap the east coast for the west, in the comics, he did so because he mistakenly fingered the wrong suspect in the Sin-Eater murders. This eventually puts him on a collision course against Spider-Man, who of course, Eddie is yet to meet in the films.
Either way, it wouldn't be difficult to bring Eddie back to the Big Apple. Have him get contacted by the real Sin-Eater, and presto - you have the perfect excuse for the character to leave San Fran, and fall right into the lap of Spider-Man.