That may or may not be the case (there are some pretty strong criticisms of the notion that we cannot know whether or not we are brains in a vat -- but let's not get into those here.), but the problem with certainty in the sciences has more to do with the fundamental nature and limits of inductive logic or reasoning than it does with the brain in a vat notion. Inductive logic (aka reasoning) is fundamental to the sciences since they rely on empirical evidence. However, inductive logic cannot by its very nature provide certainty. Hence, the sciences are ultimately uncertain.
I agree to a large extent. But there are qualifiers.
For example, no observation or measurement has infinite precision. There always *always* error bars around any measurement. But, we can, and do establish that certain results are true *to a certain approximation*. And that is something that science can establish with certainty for each measurement.
So, when we measure the length of a rod, we may not be able to say that the rod is exactly sqrt(2) units long. But we *can* determine with certainty that the rod is between 1.41 and 1.42 units long.
As far as the problem of induction: there is no certainty that the Earth will continue to rotate until tomorrow. But the probability of it failing to happen is so small that we generally ignore it.
I'd also say that you probably over-estimate the 'certainty' that comes from mathematics and logic. Whatever certainty those two subjects have come from them being abstract and having little directly to do with 'reality'. So, we can prove 1+1=2 from very few assumptions, but whether those assumptions apply in nay given physical situation is a completely different matter.