If you want to dine with a view, then one of the options is the Fort House Restaurant. It's located en route to Mattancherry, the same road as Pepper House, and is part of the Fort House Hotel complex. The restaurant has a beautiful open-air dining space by the Fort Kochi harbour and during evenings (sans the mosquitoes) it makes for a gorgeous dinner spot. Afternoons, there are usually beach umbrellas that'll protect you from the sun and pedestal fans to cool you down. But honestly, you'll forget about all of that once you catch the harbour views. Boats and ships usually pass by the harbour, so while you wait for your food, you can watch that. And of course, take plenty of pictures, like how many guests often do.
Coming to the food, the menu is heavy on Kerala seafood and it's pretty good (you'll find plenty of locals apart from tourists having a meal here). We recommend the Fish Pollichathu, Fort House Chicken Roast, and Beef Pepper for the carnivores. We didn't spot a lot of vegetarian options here. Pair your curries with staples appam, rice or Kerala porotta.