Here is a pic.

I would cut the new shoot below the ground level. All your other thinking is correct. The rootstock is much stronger and more vigorous than the scion (Meyer); if you leave it, it will grow and the Meyer will not.

if the sucker branch came from below the soil, would it be planted too deep?

I did transplant the tree in a bigger pot last year. Thats when the new shoot started. It may have been planted a little too deep.

Thanks John....
I did cut the shoot off and just in a few days, the original tree has new growth. What took me so long to cut that off. I knew it wasn't right.

Also on the pic, there are 4 other small shoots from the main tree with thorns.I just cut them off as well. I left about 3 inches. I think I should just cut them off all the way as well.

Don't know why you want to cut the other branches; but that is your choice. Nearly all Meyer limbs have thorns.

What Houston said is important; if you planted the bud union below ground, the tree will not live long; you have to keep the bud union above ground. Hard to tell from your photo; but the sucker coming from below the ground is often the result of burying the bud union/graft.