Wondering which beach is better to stay at? Ocean Beach or Mission Beach?

Mission Beach for sure. But if I were you I'd pick La Jolla, Coronado (California), or Del Mar over both of those

Depends what you are looking for. 

Ocean Beach (California) is more casual, bohemian,hostel,hippy

Mission Beach is also casual, but big Boardwalk, Belmont Park, more restaurants in various price ranges. 

Out out of those two, I would go for Mission Beach.

While I like both, for a quieter, safer stay, I would choose Mission Beach.  South Mission, which is south of Belmont Park, is quieter than the northern part, but has only a few restaurants. Parking is a challenge.  If you have a car, find a place with a private parking spot.  I agree with Candace about Mission.  Get a spot on the bay side for the quiet.  North Mission is within walking distance to several restaurants.  

Look for the area (spit of land) between the beaches.  I'm sure you know vacation rental by owner (vrbo.com)--just search there--great beach houses!

Both are great options, but to me, I prefer Mission Beach because of the easy access to the board walk for people watching and bike cruising. Stay on the bay side in north mission and then its an easy walk to all the restaurants in Pacific Beach.  The bay side is generally quieter than the beach side, but still only a very short walk to the beach. Lots of vacation rentals in Mission Beach.

No question. Ocean Beach (California)!

Ocean Beach (California) is hippy & mellow + Mission Beach is family & activity full - it depends on what you're looking for!

Better restaurants in Pacific Beach, more of a hippy vibe in Ocean Beach (California). Both have restaurants and shops to walk to