First - there's no harm in bargaining. If you like the team and believe in the company, but you think the offer is a little low, then tell them that. If you have some number in your head then ask for a little more and bargain to something closer to what you want.
3% + salary is a better offer than I've seen for a first employee. I've seen 3% with no salary and salary with a lower stake, but not both together. It means they are serious about bringing you on board and consider you more than just a first employee.
It's often possible to bargain away salary for equity or vice-versa. Given your place in the company, you could ask to be a cofounder with a higher equity stake. But be prepared for the sacrifices involved. It could mean a pay cut and you will be making a lower salary than your employees for a long time.
Older engineers tend to care more about the salary than the equity. If this applies to you, you could also bargain away some of your equity for salary. Maybe $80k a year with a 2% stake in a good company sounds better to you then $40k and a 3% stake.