"There were only a few people at the meeting," is the best option. By using the word "only", you need to specify "a few". Otherwise you could say, "There were few people at the meeting."
The difference between them is subtle. "There were only a few people.." suggests that you were expecting more people to be at the meeting than were actually there. If you say "There were few people.." only conveys there weren't many people there.
If you say "There were only few people at the meeting", you will be understood, but it is not grammatically correct.