How can I minimize or eliminate noise and vibration coming into my home?
You are entitled to the, “quiet enjoyment of your property” and your local municipalities are not exempt. 

Pump stations are basically very deep wells. When they fill up from surrounding gravity drainage systems, a LARGE pump kicks on and pumps everything to another location. As you can imagine, the pump needs to be serviced and maintained at regular intervals. Cities often skip maintenance procedures because, 1) lack of funds, or 2) lack of understanding. 

1) Cities have tight budgets and will often reduce maintenance on many items, including equipment, roofing, etc. 

2) The required maintenance is not random. There is a VERY SPECIFIC list of items to perform AND in a specific order. I doubt the work is being done or being done correctly. 

At the time of installation there was a “Maintenance Manual” prepared by the pump manufacturer and the design engineer. I doubt they can find it or that they’re following it. 

There’s little you can do to your house to solve this type of problem, but the city can give the pump an overhaul or replace it and 90% of your problems will go away. I’d contact them and see if they can help. If not, you may need an attorney.