With the advent of cruise ships Ensenada has become extremely commercial and even more gringo oriented than ever. Hussong's Bar used to be a wild old bar where anything and everything used to go. The original location is up on Avenida Ruiz, there are a couple of branch operations on Lopez Mateos, the main tourist drag through town.
There used to be a place called Barkissimo on the malecon, an old boat converted to a restaurant, it may or may not still be there. It is well within walking distance from where you'll dock. I had some pristinely good steamed clams that had been farm raised in San Quintin, about an hour south of Ensenada. Keep walking down the malecon and you'll end up at the Ensenada fish market. There are many, many fish taco and marisco vendors in and surrounding the market. Choose the vendor that looks the cleanest to you and which is the busiest and it'll probably be safe to eat there. Most of the food in Ensenada is fairly safe, tourism is one of their prime industries, they don't want people getting sick eating in town.
For fine dining there used to be a place called Manzana on, I think, Avenida Ruiz. Not sure it's still there, I've heard conflicting information. It's run by a husband and wife from Cuernavaca and D.F., both professionally trained. They've had somewhat of a struggle because most people coming to Ensenada are not looking for Mexican fine dining, but for beer and a combo plate.
Depending upon how far afield you want to go, the restaurant at Punto Moro is good, and if you're really adventurous find a way to go to Laja up in the Valle of Guadalupe, the Baja wine growing region. In fact, if your ship offers a shore excursion to the Valle de Guadalupe, take it.
The San Diego Reader has some restaurant reviews and listing for northern Baja, go to http://sdreader.com click on the link to Restaurants and then just follow the links until you get to Baja.
Enjoy your trip.