The group, a coalition including Service Employees International Union Local 1021, filed the lawsuit Thursday over concerns that the shuttles have caused an increase in highly paid workers into the city, driving up housing costs.
The San Francisco Municipal Transportation Agency says more than 35,000 private shuttle boardings occur each day.
The suit follows a failed appeal by shuttle opponents to stop an SFMTA pilot program to charge companies $1 each time they use public bus stops.
San Francisco City Attorney spokesman Matt Dorsey says his agency hasn't had time to evaluate the litigation and that it would be premature to comment on it.