Does "Bad Ass!" have a positive or negative meaning?

I've heard that this in "the last ship" and that sounded like a compliment.What do you say?

In the usage you described, the phrase "Bad Ass!" is an exclamation similar to "Awesome!", "Superb!", or "That's totally rad, brah!".

This is distinct from the usage of the term "badass" as a description of a person, such as in "Chuck Norris is a badass!", which is usually a form of legitimate praise connoting toughness, rugged independence, etc. However, the term can also be used sarcastically to demean someone, such as in "Look out, folks! We've got a badass over here!", which is commonly used in internet flame-wars against so-called "internet tough guys".

The positive meaning of "bad ass" or "badass" is derived from the somewhat dated slang usage of the word "bad", meaning "cool". For example, one might exclaim "That is one baaad ride, brother!" at the sight of one of these. Or, for another example, one might say "She's a bad mama jama!" to express that one finds a particular woman exceptionally attractive. Context is important, though, with this slang usage of the word "bad", as is the tone and inflection used when employing it in conversation. Since its usage has fallen out of favor as a go-to descriptor for all-things-exceptional, the term "bad" may be misinterpreted as a disparagement or criticism if not given the proper context or tone. The term "badass" is generally safer to use, mild vulgarity notwithstanding, as its meaning is not usually interpreted as negative.

While it suggests someone who is difficult to deal with - doing things according to their own desires, standards, and timetables - it is virtually always meant to be positive. A badass cannot be intimidated or deterred, shuns compromise, lives life to the fullest, etc.

Always positive. Although it's a combination of what sounds like two insults, I don't believe "badass" has ever had a negative meaning. The Online Etymology Dictionary traces its current meaning "tough guy" at least to the 1950s.

My observation is that using "bad" à la Michael Jackson to mean "cool" or "good" is extinct and has been for a couple decades, but "badass" is very common.