The Sea Incense was introduced in Gen 3, and until Gen 4, it only increased the power of Water type moves by 5%. In Gen 4, this was boosted to 20%. The Wave Incense was also introduced in Gen 4, and has always boosted the power of Water type moves by 20%.
The only other difference is that the Sea Incense allows Marill or Azumarill to have Azurill eggs, and the Wave Incense allows Mantine to have Mantyke eggs.
Sources: Sea Incense, Wave Incense