Since Malcesine is located on the main lakeside road, called Via Gardesana, is very well connected to buses, trains and of course taxis. In order to catch a train, there are the 62/64 line services offered by ATV which stop in both the train stations of Peschiera del Garda and Verona.
The trip to Verona takes an hour and three-quarters, with buses running every half-hour. Tickets can be bought at the one of the bars in the area or directly on the bus, paying a little extra charge.
If you like ferries, keep in mind that Malcesine is considered one of the main stops for the ferries running up and down the Garda. but note that services are reduced in winter months. This means that the other northern lake resorts, which are Limone, Riva del Garda and Torbole, are easily quick to reach.
Of course during winter services are reduced, so timetable is different and you need to check it before planning your trips around Malcesine. If you want to travel farther, you can go to Desenzano, which is reachable by boat in 4 hours or by the faster hydrofoil (which is of course more expensive) in just 2 hours, half the time. It is pretty cool, isn’t it?
As far as it concerns the airport, the most convenient ones are the Verona Villafranca and the Brescia. From Verona Airport, you need to take a bus into Verona, then change to the ATV 62/64 bus service to Riva del Garda, which stops in Malcesine. From Brescia Airport, you need to take one of the two airport shuttle buses: either into Brescia (you would then need to take a bus or train to another lake resort such as Desenzano, then change to a bus or ferry for Malcesine) or to Verona.