Where and when did the negative connotations of "manipulation" appear?

When we think of manipulating objects, we might think of a juggler, magician, chef, etc.

When we think of manipulating people, however, it almost always comes with negative connotations. These fascinate me as we're perfectly prepared to have our behaviour altered by charsimatic people, but not manipulative ones.

When I look up the origins of the word, the online etymology dictionary tells me it comes from Latin of filling the hand, to manipule, meaning a measure, to skillful handling of objects, to the skillful handling of people.

I'm also familiar with NLP, Neil Strauss's "The Game", and Cialdini's "Influence".

Was there any negative connotation of manipulation before these?

Are there any other words that carry a more definite negative that I'm not aware of?

If you're looking for a more negative word meaning manipulative, I'd say Machiavellian fills the bill. It means unscrupulously cunning and manipulative.

I'll answer your first question ("Was there any negative connotation of manipulation before these?"). Your second question seems hard to answer: how can we possibly know which words and senses you are not aware of?

In the OED the earliest citations given that have the negative connotation are this one for manipulate:

1862   T. Carlyle Hist. Friedrich II of Prussia III. xii. xi. 358   He had got his Electors manipulated, tickled to his purpose.

And this one for manipulation:

1875   W. Stubbs Constit. Hist. II. xvii. 611   The third estate..was only too susceptible of royal manipulation.

So this sense is much older than neuro-linguistic programming (1970s), Influence (2001), or The Game (2005). You might want to read about the idea of recency illusion.