cost to repair a Master Cylinder on a 2003 Lexus GX470. Is $3300.00 a high quote

Use > Estimator at the top of this page, you'll get a price for 'your' zip code! .. That's a bit too much, according to your info!..

That's a little high. The part is $2,600+ and when you add in labor you should be $100 - $200 less. That's without diagnosing the problem.