<p>I'm trying to make a water insulated 1&nbsp;cm<sup>3</sup> (1&nbsp;ml) transparent container and I bought some plexiglass, I cut and glued some pieces together but it looks really crappy and barely holds the water in. I was wondering, is there a transparent material (similar to plexiglass) that can order to 3D print the container out of it? Also, if 3D printing is not the best option, where can I order around a 100 pieces of 1&nbsp;cm<sup>3</sup> transparent water insulating containers with caps?</p>

Yes. You'll probably want to use SLA or Polyjet printers with transparent resin. For example, here's
Shapeways' page on transparent SLA
and
their page on Polyjet
(which says you need to phone them for transparent Polyjet parts as their online order system can't handle it).
FDM printing with transparent materials doesn't usually result in parts that look like transparent injection-moulded parts, because the lines of material laid down by the printer are visible. There are
some techniques to make this better
, but a printing bureau is less likely to offer this kind of special handling.
In any case, you should discuss your requirements in more detail with suppliers, and they'll be able to advise whether they offer any manufacturing processes that meet your needs. In particular, if you need your containers to be food-safe, you should mention that at the start, as it'll rule out a lot of possible suppliers, machines, and materials.