What's your address on that Howard Johnsons?
3330 rosecrans st. Right in the sea world area it looks like.
Rad. Well, you are really close to a few places. Kearny Mesa (Liberty and Excalibur) are a little out of the way but both have pretty pedestrian selections. There is no liquor at Liberty, and Excalibur has a good beer/wine set up. That said, closer to you, you have Habanos, Racine & Laramie, and Churchills.
Habanos (the closest to you) I have never been to. Why? I don't know. But my buddy used to live over there and swore by that place even though it was a little more pricey.
Churchills has a nice beer/wine line-up and a Liga account. They also carry most of the MF/Pete stuff, LFD, Illusione, etc... the patio they have can get a little crowded.
Racine & Laramie is a byo-liquor set up. The "lounge" looks like a 1800's living room and David has been throwing my buddies and I crazy deals for the past coupe of years. He stocks loads of stuff I love and loads more stuff I never knew I liked (until he gave me a stick to try). The only drawback is that he closes at 8pm. You can take your cigar across the courtyard (this is in the old town presidio) and sit on the porch at the Cosmopolitan Hotel (which looks like an 1800's hotel), but they close around 9pm.
The other option is to bring your own sticks, and hit the giant patio at Shakespeare's pub and you can get loads of liquor there - this is my local clubs weekly herf-spot (we hit it every Thursday). They won't throw you out until midnight.