I have been using my Brother PC420PRW machine to free motion quilt. It is very quiet, has needle up or down and has a 7" throat. It also has a ton of decorative stitches if you're into that kind of thing. Runs anywhere from just under $400 to $500 on line.
Amazon.com sells them and you get Brother's 25/5/1 warranty which at least I've found that my local dealer does honor if you need repairs. Walmart's on-line store also has them and is sometimes a little cheaper than Amazon.com. I've had mine for 3 years and have pushed a lot of quilts through it.
It's a great little machine. I have noticed that I have to help it along when I'm binding a quilt or sewing upholstery fabric, but I'm pretty sure that it wasn't really meant to do those kinds of jobs
LOL.
If you can spend a little more you might want to look at the Brother PQ1500s--it's a straight stitch only machine with needle up/down, thread cutter and nearly 9" to the right of the needle. I've heard it works really well for FMQ. They go for between $600 and $800 new at Amazon and a variety of other on-line Brother dealers. Sometimes you see them for sale used on Ebay, but they tend to get bid up to as much as $450 or $500, almost as much as a new one. I know several quilters who have them and love them. The PQ1500s have a much more powerful motor than the PC420 which comes in handy if you're going to be binding a thick quilt, or working with upholstery fabrics, and they can sew an amazing 1500 stitches per minute, while having a very responsive foot pedal.
Neither the PC420 nor the PQ1500 has a low bobbin indicator, but I don't think you're going to find a machine with a low bobbin indicator for under $1000 unless you can pick up a used machine.
Rob