Here's the exchange (as transcribed at a movie quotes site):
Tony Stark: And so, where are you at with names?
Howard Stark: Well, if it’s a boy, my wife likes Almanzo.
Tony Stark: Huh. You might want to let that stew a while, you got time.
It is probably just a joke: the suggested name is close to Tony's real name (which is Anthony), but kind of funny-sounding because it is so uncommon. Tony asks that they think about that for a little bit — to "let something stew" is to allow it some more time to be fully developed. Presumably that's what happens, ending up with his actual name.
The Little House on the Prairie answer is interesting, but is just speculation with no citation. Yes, that's the most widely popular example of this uncommon name, but there's no indication that anything is meant by it other than "odd sounding name that is not too far off from the actual name".
Any deep connection to other characters, setting, or plot does not really make any sense, because they didn't pick that name — if the joke were "name that isn't quite right ➡ name that is right and has a clever connection", that might make sense. But here we have "name that (maybe) has a clever connection ➡ name that is right and has no such connection". That isn't very satisfying. And Tony's reply doesn't relate to Little House either; it makes much more sense if it's just a simple "odd name, not quite right" joke.
Furthermore, there are no other big references to Little House in the MCU. If this were a clever easter egg, it seems like there'd be at least some other reference to it or joke — that's something the MCU clearly does like to do.
So, there may not be deep significance. Sure, as a comment says, there's no accidents in a production of this scale — but it also doesn't mean every bit that matches some interesting coincidence is that coincidence. We surely could come up with even more far-fetched possible references if we wanted to, but there doesn't really seem to be a reason to.
Maybe that's not as exciting as the other answer, but without any references to insight from writers, actors, or directors, Occam's Razor suggests the simplest explanation is probably the best one. And that's "that funny name is almost but not quite right".