What Makes Buildings Valuable In Puerto Rico?
The value of buildings comes from 2 sources


Providing a direct VP contribution to your strategy
Providing money to implement your strategy


As you have correctly determined there are 2 archetypes of strategies:


The Shippers
The Builders


Shipping Strategy

Obviously they try to win by shipping more goods than the other players. They will choose buildings that give them better yield and control over shipping.

Building Strategy

This strategy is based on filling your city with high scoring buildings a quickly as possible so to end the game before the shippers can play their advantage. They will try to go for at least one big building (depending on what gives them the best score).

Supporting the Strategy

Equally important to both strategies is money. Without a decent income you cannot develop either strategy. So early and mid game the focus will be on buildings that improve the yield of your trades or your chances for getting a trade. Another form of income are quarries. So building that support you in getting one are also good early choices.

What is generally not a good choice is to buy something another player wants but you don't need. Aside from the fact that most buildings exist at least twice and you can only have one, even if you can buy a coveted building from under the nose of an opponent you'll be set back just as much by that buy. The other players will thank you for it. As such, "obstructive building" is not recommended.

Generally speaking the question is not what buildings have good synergies with each other. The question is what buildings have good synergies with your particular strategy.

I suggest you browse the forums over at BoardGameGeek for more strategy on Puerto Rico. There is at least one very in-depth strategy guide there that explains the mechanics far better than I could here.