Depends upon where you plan to go.
Stay away from the state of Chihuahua right now--and out of Tijuana (travel farther south to Rosarito Beach or Ensenada instead). Other than that you should be okay (although there is a gigantic hurricane about to hit the Los Cabos/ Cabos San Lucas area in about a day or two--which makes me wonder if those resorts will all be back to normal by November).
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I would think the standard websites would be the best--orbitz, priceline, travelocity, expedia--and then the websites of the hotel chains that were already mentioned (I gave the barcelo one already, and the bahia principe one is also available).
For cheap airfares, check kayak, ita, and cheapairfares.com