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Should be easy to find. A novel. Read it in early '00s. More likely it is much older. It might be a series of novels.

A fleet of traders traveling through space from star to star. They trade technologies.

The captain of this fleet is more likely from Earth, he's mostly immortal cause he bought some medical tech on one planet.

The plot of one book was that the captain has been captured and imprisoned on his flagship.

He managed to regain the control of his fleet using some spec-of-dust-sized robots flying all over the ship and doing some maintenance, by grabbing a couple of these robots into his eye.

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This is A Deepness in the Sky, Vinge's "prequel" to A Fire upon the Deep.

The fleet forms part of a trading clan called the Qeng Ho, and the main character, Pham Nuwen, was actually the founder of the Qeng Ho trading culture. Rather than being the captain (as you might expect), however, he is living aboard the fleet under the pseudonym Pham Trinli, posing as an inept and bumbling fleet elder.

The fleet is defeated, and its crew enslaved, by a rival fleet of "Emergents". Using nanoscale technology, provided by dust-speck scale floating robots that form a distributed network, Pham works out a scheme to defeat the Emergents. Just as recalled in the question, he communicates with the robots by winking one eye, to avoid surveillence.

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    Yep, this is definitely it. Nice fast work.
    – DavidW
    May 20 at 13:20
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    Actually, the specks aren't robots, "just" microcomputers with microwave transceivers, and capability to "display" by direct stimulation of the eye when inserted under the lids (and allowed to migrate to the optic nerve). As a network, however, they give considerable computing power and surveillance capability. Great novel, BTW; also read the third one (The Children of the Sky).
    – Zeiss Ikon
    May 20 at 17:07

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