JR trains link Ise to Wakayama via the coastal Kii Peninsula line. If coming in from Osaka, a slightly cheaper and faster option is to take the private Kintetsu line.
From Osaka, Ise is serviced by Kintetsu trains. Kintetsu's Limited Express depart every 30 minutes, taking 1hr 40 mins. It costs 3030 yen for a comfortable reserved seat. Kintetsu also runs Limited Express trains directly from Kyoto.
From Nagoya, Ise is serviced by JR and Kintetsu trains. Kintetsu's Limited Express is the fastest option, taking 1hr 20 mins. It costs 2690 yen for a comfortable reserved seat. By JR line it costs 1940 yen 1hr 30 mins.
Be aware that Ujiyamada station only services Kintetsu trains, while Ise-shi station is serviced by Kintetsu and JR lines.
The cheapest option for travel between Ise and Tokyo is the overnight bus operated by Sanco, (Japanese only). It's a long trip and the comfort level is possibly below an economy class air flight but at ¥7850 (return trip ¥14130) it's around half the price of the shinkansen and train option.
Ise has no ferry terminal but from Chubu Centrair International Airport one option is to take the ferry to Tsu then a bus to Tsu Station There's one ferry every hour, it takes 40 mins and costs ¥1890. There's also a ferry to Toba. With many hotel options in the seaside town of Toba this could be a good way to start a holiday. Ise and Toba are linked by Kintetsu and JR