A clear balloon containing an ecosystem would heat up due to the greenhouse effect. If it's sufficiently large and allowed to slightly expand it could float freely in the air. Imagine closed gardens flying freely around the world.
I don't think you could get them to be consistently warm on Earth. But the atmosphere on Venus is so thick you could have a bunch of these floating above the clouds.
We're not talking superfluidic Helium here... Glass or BPA should be fine... In that case the envelop is rigid and we might at well just suck out enough air to get buoyancy.
When I was reading about Sterling engines, people talked about H2 leaking straight through the steel walls of the container. I can't find a similar reference for helium, but it's conceivable, to a non-expert anyway. No superfluidity required.
Helium doesn't need to be superfluid to leak through a lot of materials. If you are designing a ultra high vacuum system you better make sure the type of glass you use doesn't leak He. Or if you get the chance to play with a mass spectrometer you can inhale helium and observe how it leaks through your chest.
Whether it would float would depend on the equilibrium that the ecosystem gets in. For example, carbon dioxide is heavier than air, so if the ecosystem has lots of it, a balloon would have to expand quite a bit to compensate for that before it floats. And of course, any balloon must overcome its own weight before getting airborne.