Communist Manifesto, Chapter 1 should make clear that the class systems of Feudalism and Capitalism are distinct. You can find further references to this in Capital.

Really, any of his works should make clear that he saw his time as one of transition, where the bourgeoisie was still establishing its hegemony in much of Europe. The Bourgeoisie was a separate class which was in the process of overthrowing the nobility.

Bourgeoisie originally just refered to free, urban townspeople in European feudal society.

The primary difference, if we stick to "means of production" was that nobles owned land, while the bourgeoisie owned tools and workshops. Both are forms of productive capital and can be used to extract surplus value (though, initially most Bourgeoisie extracted it from themselves), but the key difference is that land is not a commodity. It's a finite resource (unless you're Dutch). This meant wealth was finite for nobles, but for the Bourgeoisie, it was something that could be created. This kicked off a series of transformations in the bourgeoisie, including the increased reliance on wage labour. This would transform the bourgeoisie into modern capitalists, and capitalism would eclipse feudalism.

So, clearly relations to the means of production as a definition for class doesn't just come down to own/work. Different forms of ownership and ownership of different things can have huge impacts. As can relationships to government, the church, and other centers of power outside the primary means of exploitation.