For instance with $r(t)=\langle t+1, t^2-2\rangle$, we can substitute it with x values and y values to get $y=t^2-2=(x-1)^2-2$ form that is easy to graph. How can we do the same for $r(t)=\langle 3,t,t^2-1\rangle$?
I managed to sub $z=y^2-1$, but not sure where to place the $x=3$ in the equation.

The usual way to represent that curve in a non-parametric way is, as already observed in other answers, as a pair of equations: $z=y^2-1, x=3$.
If one is been stubborn, a rather convoluted way to obtain a single equation could be
$$(y^2-z-1)^2+(x-3)^2=0$$
or may be
$$|y^2-z-1|+|x-3|=0$$
but those are just artificial and more complicated ways to join the two equations and should be avoided.