I would say "We didn't manage to get in at the new restaurant." "At" is the preposition we use to indicate places or addresses. When you say it this way, "in" is an adverb, not a preposition. If you said "We got in the new restaurant", then "in" would be a preposition, and the sentence would mean you got inside the physical building. That is not the thought you want to express.
You could also say "We didn't get a table in (or "at") the new restaurant." That use of "in" as a preposition makes good sense because the tables really are inside the physical building.