I am wondering, as we enter this new era of Bitcoin futures trading, will the Wall Street whales manipulate the market to their advantage.
No, but how could they manipulate the market? Buy flooding it and then selling? It would take loads of capital and they wouldn't gain that much from it.
If so is there anyway to know when they are manipulating the market?
There's really no way to know unless a Wall St. bank had a wallet address publicized and then churned their own account to try to influence the price.
The beauty of Bitcoin is that the market is truly global, meaning there are numerous "doors to the market" around the globe.
A better way to manipulate the market for ones own benefit is to take advantage of the price difference of Bitcoin across multiple exchanges. Now that we're in a thousands of dollars price level, the difference in price from one exchange to another can be as much as $1,000. So if you keep balances in multiple exchanges you can trade by taking advantage of those differences in price valuation.