I'm trying to make a water insulated 1 cm3 (1 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 cm3 transparent water insulating containers with caps?
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.
3D printing services can do this, but you'll likely have better results at lower cost through an injection molding service. You probably won't even need to go through the internet; businesses doing this are common enough you can probably put a search in Google for "Injection Molding" along with your city or community and have a number or local choices, where you can go visit them in person to talk face to face about what you need.
You could order an sla or dlp printed part(which would probably be more expensive, but also quite durable and a little more transparent). Or you could order an fdm printed T-glase print, which would come out pretty clear and not be quite as strong as sla, but still pretty good for holding water.