Talking about the income sources, the two listed would only be the initial ones and would most likely be rapidly overtaken.
First having 30,000 acres of cropland ready to harvest, plus the support structures to store it, setup right from the get-go is a huge income potential. That is sufficient to support 50 knight manors, 1,000 pounds of silver. This does not even use up all of the land in one of the three sectors.
You have another sector which you could use for more cropland, for grazing animal herds, or even more specialized production such as vineyards. While not having as immediate an income potential (unless you go with more cropland of grains), this will eventually grow to the same income potential.
You could transform a portion of the forest to orchard. Even just the outer 10% along the waterways could net you 2,000~3,000 acres of orchard. Depending on type, this would provide a standard income source of 100 pounds of silver per year.
You plan on including a Hermetic Shipyard which will allow you to support a trade fleet and fishing fleet. This will eventually grow the size of both to fairly large income sources, even if you never sell a ship. And the island itself is part of the trade fleet.
Even after deducting the land for the Towers, roads, and waterways you are going to have several thousand acres not used up by the croplands, forest, and third sector crops/grazing/vineyards/etc. This can be used for supporting industry such as rapid tree growth (to support the the Hermetic Shipyard), brewer/vintner, bee keeping (along with the sub-industry of wax/candle making and mead), meat processing (sausage, aged/cured meats), carpentry/furniture making (if you are already rapid growing trees), leather working, vellum making, etc. While many of these will be used to support the Covenant there will still be excess which can become income.
Mentioned above, but bee keeping is going to be a major activity. Bees are important for your croplands and with 30,000 acres you are going to need lots of bees. The total land needing them increases depending on the third sector and if you use any of the forest as an orchard. Lots of bees produces lots of honey and wax. You are going to be producing tons of each in short order. How many tons depends on what plants they are collecting from. On the low end, you are looking at 15 tons of honey and wax with the bare minimum hives just in the croplands (though in reality it will be closer to 750~1,500 tons of each max). On the high end you are looking at 5,000~7,500 tons of each from the grasslands if they were nothing but sweet clover. However sweet clover is to rich from most animals to graze exclusively from (cattle will develop Bloat), so the amount will be lower if the land is multipurpose.
Then you have some truly exotic income types possible. Over 90,000 acres on the underside of the island that can be used to farm undersea delicacies. Finding and collecting items from the sea floor (vis, mollusk, pearls, shellfish, ship wreaks).
You problem will rapidly shift from "how to get income" to things like "how to use all income", "how not to piss off city states and nations", and "how not to break the Code because you have to deal with mundane governments".
