I would have to agree with everyone before me. If the choice is strictly between more square footage and a second bathroom you have to take the latter. With that said, you have to consider that most larger units in town come with a second bathroom anyway. Generally speaking, a property with a minimum of close to 800 sq. ft. (some are 750 - 798) will have 2 bathrooms. The larger the unit the more bathrooms in most cases. Many 2 bedroom condos in town below 800 will offer only 1 or 1 1/2 baths.
Depending on your price range and desired location there may be 2 bdrm condos priced competitively between those with 1 baths vs. 2.
Make sure you're working with a Buyers Agent to ensure that you get the information and representation you need.