The salaries you found online are what people received after they negotiated their offers! And you mentioned you had not negotiated yet, so how did you “not negotiate properly”?
In terms of which company to negotiate with: which company do you want to work for? Which city do you want to live in? If you’re not sure, and you do get an offer with the company in Phoenix, then why not tell each company about the other offer, and begin to negotiate. With the Bay Area company, you could mention you did some research, and saw that the initial offer was lower than what you expected based on somebody with your experience and skills. Make sure that each company knows you’re excited to work for them, but that you need more information to compare the two positions (remember to consider things beyond salary, like benefits).
Remember, your job search doesn’t end until you show up for work on your first day. That intro call you just had? They need to know you are actively searching and interviewing with other companies. You can let them know that if they are interested in you, they will need to move fast (and make sure they know you are interested in them). Personally, I would say I had completed some mid to late-stage interviews, but I wouldn’t say I had offers already. Years ago I made the mistake of saying I’d received an offer, and that was the last time I ever heard from the other employer again. They may assume you have accepted the offer you received, and not waste their time.
Congrats on the offer, by the way!