When I visited New York a few years ago, maybe 1998 or so, I went to
see a show. It was a very small theatre, a giant glass box on stage
(like an aquarium, but just with water, no plants or anything). The
performance was puppeteers moving silk scarves around the water. The
scarves danced, like ballet. No words, just set to Berlioz music.

What was it?

I am certain that what you saw was Basil Twist's "Symphonie
Fantastique," which was presented at HERE Arts Center in Soho in 1998.
The show, considerably enlarged, was revived recently at Dodger
Stages.

"Basil Twist and his company made waves throughout the theatre world
when Symphonie Fantastique debuted at HERE Arts Center in Soho, and
word of this sold-out sensation rippled through the city and then,
around the globe. Now this underwater creation is about to return to
New York at DODGER STAGES.

Your ears won't believe your eyes, as a remarkable team of puppeteers
orchestrate an hour-long rhapsody of mirrors, feathers, fabric,
bubbles, color and light all in a 1,000-gallon tank. Music, theater,
dance and abstract art collide in kaleidoscopic concert of forms, and
the result 'boggles the mind' says Ben Brantley in The New York
Times."

Dodger Stages: Symphonie Fantastique
http://www.dodgerstages.com/5-symp.htm

"The dictionary defines a puppet 'as a small figure of a person or
animal, having a cloth body and hollow head, designed to be fitted
over and manipulated by the hand' also 'as a figure having jointed
parts animated from above by strings or wires.' True to his surname,
Basil Twist has given the definition a new twist. The way he sees it a
puppet is 'something animated' and 'the trick of puppetry is making
something seem alive or calling the life out of something.'

According to Twist's definition, Symphonie Fantastique is indeed a
puppet show. A rather abstract one to be sure with its 180 puppets or
animated 'things' (fabrics, feathers, glitter, vinyl, plastic dyes,
etc.) manipulated by Twist and four other puppeteers through a 1,000
gallon water tank to illustrate Hector Berlioz's fevered five-part
symphony inspired by his obsessive pursuit of the woman he eventually
married."

Curtain Up: Symphonie Fantastique 
http://www.curtainup.com/symphoniefantastique.html

"This is a new, larger production of Symphonie Fantastique, Basil
Twist's underwater puppet spectacle, which premiered in 1998. This
description is from the press materials: 'Symphonie Fantastique
combines the magic of puppetry with the powerful suggestions of dance,
film, and art, set to the five movements of Hector Berlioz's hour-long
19th century classical composition. Out of view of the audience, five
puppeteers swirl fabrics and feathers, glitter and vinyl, plastic,
dyes, bubbles, fishing lures, and flashlights through the 1,000-gallon
water tank.'...

Symphonie Fantastique, which originally opened at the HERE Arts Center
in 1998, is surely the world's first abstract underwater puppet show,
making Twist the genre's undoubted standard-bearer."

The New York Theatre Experience, Inc.: Symphonie Fantastique
http://www.nytheatre.com/nytheatre/symph496.htm

Google search strategy:

Google Web Search: basil twist "symphonie fantastique"
://www.google.com/search?hl=en&q=basil+twist+%22symphonie+fantastique%22

If I have misidentified your show, or if anything is unclear or
incomplete, please request clarification; I'll be glad to offer
further assistance before you rate my answer.

Best regards,
pinkfreud

Spot on.