We stayed at the Comfort Inn in Old Town. (I have their discount card. If you don't, you can join for free too.)
We also have stayed at the Best Western on Coronado Island.
And a third, a Super 8 on Rose Cran, that was cheap. We got what we paid for. (The plus -- there was a Starbuck's next door.)
Of these three, the Comfort Inn was nice and reasonably close to the zoo.
The only downside for us was I think they thought they were doing us a favor by giving us a bay view room. It was more of a soft industry view room over the main interstate. (Noisy) So no great room views there, but the rate was reasonable and the room was newly remodeled and clean, and easy access to the main highway.
There are nicer hotels down the street that are higher priced but more for the tourist staying directly there.
If you belong to AAA, you should pick up one of their guide books. I have one on hand if you want me to look up anything.
The Zoo is in Balboa Park, and I don't recall seeing any chains directly in that area.
AK : Lions, Tiggers & Bears! Oh My!
CSR: 01/01
DL- off site: 05/01
WDW - on site: 01/02