Can I use different data vendors between TWS and Ninja Trader interface?

Yes. It should be noted that Ninja Trader does not operate as a vendor of market data and use of this application requires provision of data by a third-party connectivity provider. While IBKR can serve as this provider for real time prices, these prices are not provided on an unfiltered tick-by-tick basis, a prerequisite for fully populating Ninja Trader charts.  Therefore, a common setup is to use Ninja Trader as a front-end order entry platform and route orders to TWS for execution and clearing by IBKR, then bridge to a third-party vendor for market data.

Additional Information

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Compatibility between IBKR and MetaTader
Is Ninja Trader compatible with Trader Workstation (TWS)?
Is Ninja Trader compatible with IBKR's Financial Advisor, Family Advisor and Non-Professional Advisor account types?
Can orders submitted through Ninja Trader for execution through TWS be monitored with TWS?