My wife and I have US passports and are flying into Ercan airport in Northern Cyprus. We'd like to cross the border in Nicosia and spend some time in Cyprus. I know this is in question because the Republic of Cyprus doesn't recognize Ercan as an official port of entry. I've also heard that for US passports the guards can stop you but almost always let you pass. Can anyone confirm this is the case or give me more information?
Legally speaking, no, you can't. The Republic of Cyprus's (ROC) position on this is clear: the Turkish occupation of the northern half of the island is illegal, and they do not recognize the Turkish Republic of Northern Cyprus's (TRNC) authority. Therefore, if you enter Cyprus via the TRNC, you are an illegal immigrant as far as the ROC is concerned and subject to detention and deportation if caught.
However... in practice, the ROC only appears to apply this to people who require visas for the ROC. If you are a citizen of a country that does not require a visa for the ROC, including the USA and Australia, you are generally permitted to enter the ROC without consequences. (Exception: you are not allowed to fly out via the ROC, but must return to the TRNC. I presume this is because otherwise the Immigration computers would barf.)
EU/EFTA citizens enjoy freedom of movement in the ROC, and so they cannot restrict or penalise you even if entering the island via the TRNC and exiting via the ROC.
All things considered, it's preferable to visit the other way around, namely from the South to the North. Here the geopolitics work the other way: the ROC claims the entire island, so once you've legally entered they allow you to visit the North (because they pretend it's ROC territory), and the TRNC has no claims on the southern half of Cyprus, so they're happy to let you enter "officially" as well.
Don't fly into Ercan Airport, because you will be breaking the law of an EU member nation-the Republic of Cyprus. It's a matter of ethics, not practicality. On top of it, flights into Ercan Airport are not controlled by the International FAA rules and procedures, so safety is a concern as well. Those airlines that do fly into Ercan routinely ignore Flight Traffic instructions issued by the IFAA certified Air Traffic Controllers in Cyprus. How safe does that sound to you? (I am a licensed Private Pilot with Commercial and Instrument Ratings).
If you fly into Ercan and attempt to cross the border into ROC you MAY be turned away, so why do it? Fly into Larnaca Airport and take a taxi or bus to Nicosia. If you want to cross over into Turkish Military Occupied Cyprus, you can do so without issue. And legally.
The whole issue of travelling into Turkish Military Occupied Cyprus is grey-area legally, I don't know why people do it. The beaches in South Cyprus are much nicer, the accommodations vastly superior, they use an internationally recognized currency-the EURO and their legal structure and laws are based on European Court of Justice rulings. The KKTC (Turkish Occupied Cyprus) is a quasi-military nation controlled by a regime that answers to Ankara. Their laws are whatever the regime says they are on a daily basis. Who needs that?