Flight
Flying to Merida International Airport is the most convenient way to travel. After your arrival, you can take a taxi to your hotel destination. Uber service is available in the city.
Flight
Flying to Cancun is usually a cheaper option. After your arrival to Cancun International Airport, there are two options to travel to Merida: you can either take a bus from the airport directly to the city, or you can first take a bus (or taxi) from the airport to Terminal de Autobuses ADO Cancun (downtown) and then take a bus to the city.
House Or Rental
Airbnb may be a great option for lodging. A friend of mine rents a house in the beautiful downtown Merida through that app. Feel free to contact her if you are interested (see link).
Hotel
There are several good options for hotels in Merida (see link). Downtown hotels can give you the advantage of having lots of touristic places to visit within walking distance.
Rental Car
If you are planning to visit touristic places around the Yucatan Peninsula, then the most convenient way to commute is by renting a car.