w/ boundary
is as good as it's going to get.
Then:
let $M$ be a manifold w/ boundary....
Short of inventing your own I cannot see one. However it isn't wrong to invent your own as long as:
- It makes sense (it isn't the product of an insane and troubled mind)
- YOU STATE IT AT THE FIRST OPPORTUNITY
For example:
Here $\mathcal{B}$ shall mean a manifold with boundary, for example:
- Let $\mathcal{B}M$ be a manifold
Tells us this is a manifold with boundary
But I'll be honest, that doesn't seem great. It's only worth it if you write this A LOT on the same thing IMO.
Initial answer
At first I said to use this:
Let $\partial M$ be a manifold
While this implies that $M$ has a boundary, it isn't the most obvious. Make it clear at the start you use $\partial M$ to denote a manifold with boundary if you use this.
I don't like it because the boundary of this manifold is then $\partial\partial M$ unless you assume $M$ denotes the not-boundary part and $\partial M$ the boundary.