Yes: If you are substantially delayed getting to JFK, you probably won't be "protected" for missing your flight to BUF. Depending on the no-show policies of the JFK-BUF airline (and the type of fare purchased), you might have to purchase last-minute tickets to BUF, and might or might not receive a credit for the flight you missed.

Have you priced LIH-BUF on other carriers?

Have you priced a ticket to a nearby airport like ROC or YYZ to see how it compares? A one-way car rental from either of those airports to Buffalo might be a cost-effective alternative.