There are several ways to get into San Carlos.
By ship
You can cross into Nicaragua from Costa Rica getting a boat in Los Chiles. Leaves at 1 pm in Los Chiles and costs 5000 Colones / 180 Cordobas or 9 US $ You will arrive in San Carlos at around 3 pm not so many options left to leave Sna Carlos on the very same day
You can get into by boat from Isla Ometepe or from Granada. The Ferry leaves Granada at 2 pm on Monday and Thursday. It stops by in Altagracia at the Isla Ometepe where it leaves at around 6 pm.
There are boats coming in from El Castillo and San Juan Del Norte.
There are boat conactions to Solentiname Islands and to the towns on the souther shore of the Lake of Nicaragua.
By bus
There are buses to and from Managua. The trip takes 7 hours due to the road conditions occasionally you will have to leave the bus so that it makes it up the hill
By plane
There are daily flights from Managua ~120 US Round Trip