The 90 days refers to telephone support, and yes, you're eligible for it if you buy from Best Buy.
If you buy AppleCare, the 90 days of telephone support is extended to three years (from the date you purchased your MacBook Pro), along with the included hardware warranty.
If you ever need help (regardless of your telephone warranty status), you can make an appt at the Genius Bar, assuming you have an Apple Store nearby. It's free.