Hi, Emily! Halloween time is really fun at Disney. Make sure your 3 year old brings a Halloween costume for Mickey's Not So Scary Halloween Party!
Since you want to visit
Downtown Disney during your vacation, I recommend staying at
Port Orleans French Quarter. From this resort, you can take a boat that drops you off right at Downtown Disney where you can go shopping or enjoy a wonderful meal! Port Orleans Riverside is next door to the French Quarter, but there is less walking at French Quarter which might be nice with a 3 year old.
To get to Chef Mickey's (Contemporary Resort) from Port Orleans French Quarter, take the bus to the Magic Kingdom. From here, you can either take the monorail and get off at the first stop, or simply take the walkway from Magic Kingdom over to the Contemporary (about a 10 minute walk.)
Have a fun Halloween in Disney World!