Update of Nov 10, 2016:
Unfortunately the answer to the question as it stands turned out
to be negative. -- These days I found a counterexample: put
$$
G := \langle \tau_{0(2),1(2)}, \tau_{0(2),3(4)}, \tau_{4(9),2(15)} \rangle.
$$
Then all integers $0, 1, \dots, 87$ lie in one orbit under the action
of $G$ on $\mathbb{Z}$, but $G$ is not transitive on $\mathbb{N}_0$
since $88$ lies in another orbit.
The crucial feature of this example appears to be that intransitivity
is forced by the existence of a nontrivial partition of $\mathbb{Z}$
into unions of residue classes modulo $180$ which $G$ stabilizes setwisely.
The modulus $180$ happens to be the least common multiple of the
moduli of the residue classes interchanged by the generators of $G$.
This suggests to reformulate the question as follows:
Question (new version): Let $G < {\rm Sym}(\mathbb{Z})$ be
a group generated by $3$ class transpositions, and let $m$ be
the least common multiple of the moduli of the residue classes
interchanged by the generators of $G$. Assume that $G$ does not
setwisely stabilize any union of residue classes modulo $m$
except for $\emptyset$ and $\mathbb{Z}$, and assume that the
integers $0, \dots, 42$ all lie in the same orbit under the action
of $G$ on $\mathbb{Z}$. Is the action of $G$ on $\mathbb{N}_0$
necessarily transitive?
Remarks:
If true, the assertion is still sharp in the sense that the
bound $42$ cannot be replaced by $41$ (cf. the first remark
on the original question).
It is conceivable that the assertion needs to be further weakened
a little by assuming that $G$ does not setwisely stabilize any
union of residue classes except for $\emptyset$ and $\mathbb{Z}$.
(Also in this case a positive answer to the question would
still imply the Collatz conjecture.)