I've done some research on this topic myself. I would like to be a freelance makeup artist in addition to having a full time job. There are a lot of online schools, which are not as looked highly upon as in person courses, but they are still very good and better than nothing.
http://www.robertjonesbeautyacademy.com/ This is probably the cheapest, yet decent online program. They do send you certificates though, which you can show to people you are being interviewed by, that may help somewhat. (I now work at a makeup counter & proudly brought my certificate from here in.) I think it's three hundred something and you have the opportunity to get novice, master, & pro certificates.
http://www.hexmakeupartist.com/ Hex has an excellent long distance learning program. I've heard excellent things about it and want to try it, but it is pricey. The long distance program is like around 1,700 without the makeup kit.
http://www.qcmakeupacademy.com/brochure.php?source=ADWORDS_MA_US&gclid=CN6n1OuZ8LECFQJx4Aod3QQARw QC Makeup Academy is also widely respected with a pretty big following. It's online, and has Master Makeup Artistry which is more money and Makeup Artistry which is around 1,500 the last time I checked. But don't quote me on that price, i'm not 100% sure. Lol
http://www.jeanmadelinemakeup.com/Jean_Madeline_Academy_of_Makeup/JAM___Home.html JAM has an awesome in person program if you're in the Philadelphia area.
http://www.cosmixinc.com/ Cosmix seems extremely good if you're in the Florida area.
There are also a bunch of in person courses being offered in California, if you're by that area.
http://lastlooksmakeup.com/ Last Looks travels to different busy states and citys. They offer professional courses.
And last but definitely not least
http://www.makeupschool.com/ Makeup Designory. They are probably one of the best makeup schools in the world. (It's only in person, just so you know.) It's probably one of the only makeup schools that is not just courses, it's actually like "school, school". (Sorry it's hard to explain.) You actually get a schedule (like 5 days a week) and most of the programs are at least six months, if not a year. It seems kind of competitive but I'm sure it would open a lot of doors. It's very pricey though. I think the Master program artistry program costs over 20,000 dollars though. So I'd only enroll if you are very, very, serious about this. It's in New York City, but there's also one in LA by the way. I ordered a pamphlet from this school.
By the way, you can also take an esthetician program, that a lot of beauty schools will offer which is basically like skin care with some makeup. Or you can get a cosmetology license that kind of covers some makeup from Empire Beauty school or wherever. It will be well respected, since it covers some makeup. HTH