As a (hopefully fun) exercise, we show that the problem is complete for $\Pi_2$ (under many-one reductions).
That is, equivalent to determining whether a given TM halts on all inputs.
(This is strictly harder than the halting problem.)
Let $x$ be a given computable number (encoded as defined in the post).
Lemma 1. The problem of determining whether $x$ is transcendental is complete for $\Pi_2$.
The proof builds on this answer,
which shows that determining whether a computable number is rational is $\Sigma_2$-complete.
Per OP, a computable number $x$ is encoded as a TM $B$ that
enumerates the bits of (the fractional part) of $x$ in order.
Specifically, letting $B_i$ denote the $i$th bit enumerated by $B$,
the number encoded by $B$ is $x(B) = \sum_{i=1}^\infty B_i\,2^{-i}$.
(For ease of presentation, we restrict to numbers $x\in [0, 1]$.)
Let $A$ denote the problem of determining whether $x(B)$ is algebraic, given (the encoding of) $B$.
Any number is transcendental iff it is not algebraic.
Let $\overline A$ denote OP's problem, of determining whether $x(B)$ is transcendental.
Hardness result: $\overline A$ is $\Pi_2$-hard
We show this by reducing the following problem to $A$ (the complement of $\overline A$).
Problem $F$ (for "finite"). Given (the encoding of) a TM $M$ that enumerates a sequence of bits, is $\sum_i M_i$ (where $M_i$ is the $i$th bit enumerated by $M$) finite?
Problem $F$ is easily shown to be $\Sigma_2$-hard.
(For a proof, see Claim 1 of this answer.)
Given an input $M$ for $F$, the reduction will produce a TM $B$ such that
$$x(B) = \displaystyle\sum_{j=1}^\infty M_j\, 2^{-j!}.$$
Specifically, the TM $B$ enumerates the desired bit sequence as follows:
TM $B$:
- for $i\gets 1, 2, \ldots,$ do:
- $~~~$ if $i = j!$ for some integer $j$, output $M_j$, else output 0
To show that the reduction is correct, we show the following claim:
Claim 1. $\langle M \rangle \in F$ iff $\langle B\rangle \in A$.
If $M$ outputs finitely many ones, then $B$ does as well, so $x(B)$, being the sum of finitely many rationals, is rational.
This shows the forward direction of the claim. We show the converse as follows.
NB: This part is adapted almost verbatim from a related argument by Yuval Filmus.
Assume for contradiction that $\langle M \rangle \not\in F$
(that is, $\sum_i M_i = \infty$) but $x(B)$ is algebraic.
Since the binary representation of $x(B)$ is aperiodic, $x(B)$ is also irrational,
and we can apply Liouville's criterion with $\alpha=x(B)$:
Lemma. Suppose $\alpha$ is an irrational algebraic number. There exist integers $C,n$ such that for all integers $p/q$, $$\left| \alpha - \frac{p}{q} \right| \geq \frac{C}{q^n}.$$
For a proof see e.g. Wikipedia.
Fix such a $C$ and $n$ from the lemma, for $\alpha=x(B)$.
Let $r$ be an arbitrarily large integer, $r \gg n$.
Taking $q=2^{r!}$, by the lemma, we have
$$ \frac{C}{2^{r!n}}
\le
\left| X(B) - \frac{\sum_{i=1}^r M_i 2^{r!-i!}}{2^{r!}} \right|
=
O\left(\sum_{i=r+1}^\infty 2^{-i!}\right)
=
O\left(\frac{1}{2^{(r+1)!}}\right)
=
o\left(\frac{1}{2^{r!n}}\right)$$
(as $r\to\infty$).
This is a contradiction.
Hence, $\langle M \rangle \in F$.
This completes the proof of Claim 1.
So $A$ is $\Sigma_2$-hard. It follows that its complement $\overline A$ is $\Pi_2$-hard.
Upper bound: $\overline A$ is in $\Pi_2$
To show this we will show the equivalent statement that $A$ is in $\Sigma_2$.
Given a computable number $x(B)$,
define $x_u(B) = \sum_{i=1}^u B_i 2^{-i}$,
so that $x(B) = \lim_{u\to \infty} x_u(B)$.
Given also a polynomial $p$, for $m\ge 1$, let $N(p, m)$
be computed as follows:
Compute a bounded interval that $x(B)$ lies in.
(By our definition of computable number, we can take this interval to be $[0,1]$, but this step should be possible with any reasonable definition.)
Compute a finite upper bound $D$ on the absolute value of the derivative of $p$ within the bounded interval. (E.g., assuming the interval lies in $[-X, X]$ and $p(x) = \sum_{i=0}^d p_i x^i$, take $D = \sum_{i=0}^d |i p_i X^{i-1}|$.)
Finally, take $N(p, m)$ just large enough so that $D/2^{N(p, m)} \le 1/m$.
Note that by the choice of $D$, we have (for all $p\in P, m\ge 1$)
$$
~~
|p(x_{N(p,m)}(B)) - p(x(B))|
\le
D|x(B) - x_{N(p,m)}(B)|
\le
D/2^{N(p, m)}
\le
1/m.
~~(1)$$
Let $P$ be the set of single-variable polynomials with integer coefficients.
Claim 2. $x(B)$ is algebraic if and only if
$$
~~~~~~~~~~~~~~~~~~~~~~~~~
(\exists p\in P)~(\forall m\ge 1)~|p(x_{N(p,m)}(B))| \le 1/m.
~~~~~~~~~~~~~~~~~~~~~~~~~(2)$$
To finish we prove the claim.
(The claim implies that $A$ is in $\Sigma_2$,
because $p(x_{N(p,m)}(B))$ is computable given $B$, $p$ and $m$.)
Now suppose that $x(B)$ is algebraic,
that is, $p(x(B)) = 0$ for some $p$ in $P$.
Then (2) holds because, for this $p$ and all $m\ge 1$, by (1),
$$|p(x_{N(p,m)}(B))-0| \le 1/m.$$
Conversely, suppose (2) holds.
Then for some $p\in P$, by (1) and then (2),
$$(\forall m\ge 1)~~|p(x(B))| \le |p(x_{N(p,m)}(B))| + 1/m \le 2/m,$$
so $p(x(B)) = 0$. So $x(B)$ is algebraic.