So I suppose that poor American Ballet Theater (ABT) doesn't stand a snowball's chance, as it does not have an academy that feeds young dancers to its company? But wait -- some of the so-called Top Five/Six employ an inordinately high percentage of dancers (especially soloists and principals) who graduate from academies all over the globe. I am particularly thinking about the Royal Ballets of England and Denmark. Yes, they have schools but employ about as many 'foreign' dancers as does ABT in the United States, i.e., non-Britons in Britain & non-Danes in Denmark. By that argument, American Ballet Theater is definitely in the top Five or Six troupes today.
If one wants to look to national purity as a benchmark for the Top Ballet companies, then only four truly-greats remain on this earth: Kirov-Mariinsky, Paris Opera Ballet, Bolshoi and New York City Ballet, although every single one of those troupes has at least one 'foreigner' in its ranks. And hot on their heels are Chinese, Korean, Cuban and Japanese troupes that indeed retain national purity in their ranks, plus have wonderful academies. They fall short of the list only because they are relatively young, compared to the others. In the case of Cuba, the current economic situation is an additional problem...but don't count those Cubans out, in the longer run!
Edited to add my rankings (duh...):
1. Kirov-Mariinsky - The One, The Only, To the Manor Born by Imperial Decree of the Romanovs. There is only one Mecca in Islam and there is only one 'Mecca' in Ballet and it's an aqua-and-white building on Theater Square in St. Petersburg!

Just because an oddity (Somova) or two appear in the ranks every now and then is no reason to lower its status. Beyond the mystique is the Elegance & Carriage that the Bolshoi can't match. Never has - never will. Unparallelled corps de ballet in the classics. Amazing soloists that just keep bubbling up from the Vaganova Academy, year after year, century after century.
2. Paris Opera Ballet - fabulous precision, especially in the legs & feet. Best Feet Trophy! Wonderful mix of repertoire, too. To think that 30 years ago -- before Nureyev -- they were rarely on anyone's Top 10 or even Top 20 list.
3. Bolshoi - Excitement Factor. Trophy for Best Overall Improvement during the last 3-4 years.
4. New York City Ballet - general unity of style & incomparable repertoire outside the classics.
5. Royal Ballet of England - currently the best among a group of companies that I call "The Eclectics" -- those that draw dancers from around the globe more than from its feeder schools AND employ a huge number of International Competition Winners. ABT and RDB are the others - and they round-out my Top Seven.
Among American troupes that I've seen, I'd definitely add the Joffrey to NYCB and ABT to round-out the Top Three, due to the Joffrey's wonderful repertoire and high-quality in dancers who represent many body types and styles. I've also admired, recently, Pa Ballet, Boston Ballet and Miami City Ballet. I suspect that San Fco and Pacific N Ballets also rank right up there, from what I've read and heard.