First of all, there's only one modern polite word to call a foreigner and it is 外国人. There are other phrases too, such as 海外の人 or 海外の方. The latter one is used more often.
However, you mostly hear 外国人 when a politician talks from a tribune or an overly politically correct Japanese person tries to be polite.
In fact the normal way to refer to a foreigner is 外人 and there's zero offence in it. When talking about a particular person, -さん is added, making 外人さん. Again, this is not offensive even a bit and is hardly ironical. I'd say it is quite polite way to refer to a foreigner even if not suitable for an official setting.
And of course there were always foreigners who feel offended by the 外人 word because apparently the word is made of "outside" and "man" and with some fantasy can be translated as an "alien". Which is well, quite true, so I see no reason to be offended here.
Alien is perfectly normal word to refer to a foreign national or to a foreign introduction.