Yes, "next to" or "by", but be friendly.
Please wait next to that table.
Is a kind of minimal sentence. It communicates what you want to say, but it doesn't make people feel very welcome.
Why are you asking them to wait next to a table? What are you going to do while they wait? How long will they need to wait?
Two lattés and one americano to go? Okay! If you can just wait a minute over by that table, I'll bring them right over for you.
Don't worry about confusing with being a waiter. The customers know that they aren't waiters. But don't use "wait on that table", which is the idiomatic preposition for being a waiter.